Babette's Plague
by Kellifer
Summary: The Atlantis team fails to check in and it's up to SG1 to see just what the hell is going on. JD S9 Crossover with Atlantis. COMPLETE.
1. Chapter 1

"How long has it been?"

General Landry was standing in the control room overlooking what he now thought of as his Stargate and looking from one wide eyed late night technician to the other. Both looked nervous as hell and like they'd personally been responsible for what had occurred.

He enjoyed the 'gate technicians probably more than the rest of his current staff. They were so easy to terrify. Just the right kind of stern look and they scampered.

"Um…ah, I mean," Peters looked through the paperwork spread across his workstation, probably looking for any kind of evidence of the last transmission they had received from the Pegasus Galaxy. His searching grew more frantic with each passing second and Hammond decided to be gracious and let the boy off the hook.

After all, the report he was desperately searching for was on Landry's desk.

"About twelve hours overdue." Landry looked up and spotted Walter bustling into the control room, the offending report in hand and with a reproachful look on his face. Landry inwardly groaned. Walter would be finding subtle and almost indefinable ways to torture him about the mistreatment of his techs for days.

With the figure said aloud though, Landry forgot his gentle teasing and focused on the problem at hand.

"Twelve hours?" he repeated, raising eyebrows.

"Twelve hours what?" Samantha Carter appeared at his elbow as if by magic. He wondered if maybe she had felt a subtle disturbance in the 'force'. He also decided that Teal'c's passion for the Star Wars movies was getting out of hand if even _he_ started thinking in Star Wars metaphors because he'd had the movies inflicted on him so many times.

"Apparently Doctor Weir is twelve hours overdue for filing her report. She's been late before, but never by this much." Landry explained, turning slightly to include Sam in the discussion. A frown was already creasing her brow and he held up a placatory hand. "It doesn't mean anything yet. They could have a malfunction on their end or someone is late filing a necessary report that they need before they send everything through. Remember, they're limited to how many times they can send through a communication and they're not going to dial us to tell us they're running late."

Sam crossed her arms and cocked her head at Landry and he sighed mightily, scrubbing a hand over his face.

"I know, something's wrong isn't it?" he conceded and Sam's mouth firmed as she nodded.

xxxxxxx

After nine years, Daniel Jackson barely resembled the shuffling and lanky geek he had once been. He was as comfortable with firearms as any trained marine and could handle himself easily in hand to hand. He cut off long hair, toned his muscles and would meet people's eyes when he walked the hallways of the SGC rather than looking at his shoes.

Despite all this, Jack O'Neill could still sneak up on him.

Jack stalked behind Daniel silently and raised a hand, grinning. He waggled his fingers just out of Daniel's peripheral vision and then curled his thumb and middle finger until they met. He positioned his hand carefully and then let go, flicking Daniel in the ear.

Daniel yelped in surprise, his hand darting out across his desk and snagging the first thing it came into contact with. He spun, holding a fertility statuette from P3S-989 with a rather prominent member, above his head.

Jack was already doubled over, laughing his ass off.

It took a few seconds for Daniel to release his grip on the statuette and lower it, letting his breathing also get under control. "Jack, for chrissakes!" he snapped, jabbing Jack in the chest with the statuette. "You almost gave me a heart attack." Jack relieved Daniel of his 'weapon' and looked at it, turning it over in his hands.

"You touching me with this thing doesn't mean we're married does it?" he asked, his brow arching. Daniel snatched the statuette back and stretched over to his bookshelf, placing it out of harms way.

"No, but you might now be pregnant," he snarked, but his scowl dissolved into a grin only seconds later when Jack used the sleeve of his dress blues to wipe his streaming eyes and nose. "That's disgusting Jack," he remarked, but yelped and danced out of the way when Jack shrugged and made a grab for Daniel's own sleeve.

"I've gotta get it dry-cleaned anyway."

They both stood, looking warily at each other for a few moments, breathing heavily, Daniel recovering from his fright and Jack from his giggles. They both grinned and Jack punched Daniel in the shoulder affectionately. "Should we start again, this time like normal people?" he asked and Daniel snorted.

"You've never been normal."

"Quiet you," Jack waggled a finger. "I'm being serious. Now, hello Daniel, how have you been?"

Daniel reached for his coffee cup on the desk behind himself and grimaced when he found the contents cold. "Not too bad. What brings you here?"

"Apparently we've lost contact with Atlantis. The big wigs are worried," Jack said and Daniel, who'd been contemplating taking a sip of the stone cold coffee anyway because it was caffeine and nearby, lowered the cup.

"We have?"

"My God, Daniel. Do you ever leave your office short of going off world or to the bathroom?" Jack demanded, relieving Daniel of the offending mug that Daniel had been staring into again. He took it over to the small sink in the corner of Daniel's office and dumped out the contents, rinsing it quickly and setting it aside.

"Ye-es." Daniel grimaced, knowing his affirmation sounded false ever to his own ears. He always assumed when something exciting happened Sam or Teal'c would come and let him know, unless they were involved with fixing the problem.

He always found out, but usually got the cliff notes version after the excitement if he wasn't actively needed.

"Doesn't anyone come and chase you out of this office?" Jack grumped and Cameron Mitchell appeared in the doorway as if on cue, dressed in a t-shirt and track bottoms and with a basketball under his arm.

"Dannyboy! Time for natu-" He started when he noticed Jack and came to attention, the ball falling from under his arm and rolling away down the hallway. "Sorry, Sir," he said, snapping a salute.

Jack sighed and waved a dismissive hand at him. "At ease," he said.

"Did you know we'd lost contact with Atlantis?" Daniel asked, rounding his desk.

"Yeah. The techies are working on it. I'm sure they'll let us know if they need us," Cameron supplied and Daniel raised his eyebrows at Jack.

Jack scowled. "When something happened, I was always in the control room," he said.

"Doing what?" Jack wasn't sure if Cameron was teasing and had the best deadpan face in the business, or if he was genuinely curious.

"Important…stuff." Jack said, waving a hand.

Daniel's phone shrilled and Jack thought saved by the bell was the appropriate response. Daniel leaned over his desk and snagged the receiver out of its cradle, his expression growing serious. "Yes, sir," he said, raising eyebrows at Jack again, but this time Jack had the feeling he was being included in something. "I don't have to ask him," Daniel added and Jack's interest was well and truly perked. He leaned sideways, trying to catch the other side of the conversation, but Daniel leaned away on the other side as far, almost comically overbalancing. "No, I don't think it's his call." Daniel's brows had drawn down and he was looking at Jack sternly.

Jack knew the look. Daniel was angry with Jack for something he hadn't even had a chance to _do_ yet.

"No, I don't think that's-" Daniel sighed theatrically and then handed the receiver over to Jack, his scowl firmly in place.

Jack placed the receiver to his ear and then looked at Daniel, his eyebrows climbing his forehead in a quest for his hairline. Cameron watched both men, fascinated by the interplay between them.

"Absolutely not." Jack snapped, and Cameron had to admit that now he was fascinated, just as Daniel snapped out a plaintive "Ja-ack!"

Jack listened to the person on the other end, nodding every now and then, a habit that Daniel teased him mercilessly about. He finally looked up at Daniel and exhaled. "I _do_ understand that. Everybody keeps telling me that…. No, of course not but… alright, yes, I do get that, however… alright fine, but if he goes, I go… oh, right." Jack pulled the receiver away from his ear, looked at it for a few beats, and then dropped it into Daniel's outstretched hand.

Both Daniel and Cameron were watching him.

"Okay, now both of you know what's going on and I'm in the dark." Cameron grinned.

"They want Daniel to go to Atlantis," Jack supplied, looking a little bewildered.

"I guess that makes sense if something's happened. He is the foremost-"

"Don't say it," Jack growled and Daniel tried to hide his grin behind his hand but only managed to make it more obvious.

"It's my call Jack," Daniel protested. "I want to go. I want to help."

"You want to see what all the fuss is about," Jack corrected and Daniel shrugged, not denying it.

"Anyhow, apparently this is over my head," Jack held up his hand when Daniel's face broke into a grin that spread from ear to ear. "I thought saying that you couldn't go without me would be a deal breaker."

Cameron looked from Jack to Daniel and back again.

"And?" he prompted.

"They said they'd assumed I'd be going. Something about how Hammond had taken the Prometheus out and they figured it would only be a matter of time before I wanted to do the same with the Daedelus."

"So, we're-"

"Going. Pack a bag."


	2. Chapter 2

"You'll be alone."

"I'll be fine."

"But… alone."

"I know. I'll still be fine."

"I was hoping-"

"We both agreed that if you got any worse you'd go to sleep, just like everyone else."

"I feel fine, really."

"I don't believe you at all. We agreed. I'll be okay."

"But… alone."

"Go to sleep. I'll be here when you wake up."

xxxxxx

There was a thump and a cry from just outside the cramped quarters they were sharing and Cameron looked up at Sam with his eyebrows raised. "What was that?" he asked, starting to rise, but Sam waved him back down.

"My guess? The General is bored."

Cameron's eyebrows only got higher and he stood again, leaning around the doorway. He looked back at Sam who hadn't even bothered to raise her eyes from her laptop.

"See?" she said smugly.

Cameron leaned back out into the hallway and caught Daniel glaring at him. He had apparently been ambushed on his way back to their quarters and was now standing with Jack pinning his arms behind his back, holding him at an uncomfortable looking angle. "Little help?" Daniel demanded but Cameron held up his hands.

"I'm not messing with a General," he replied, his tone trying for apologetic but he couldn't hide the smirk in it.

"You'll keep," Daniel growled, but the threat lost its impact considering Jack chose that moment to switch grips so that Daniel was in a headlock and having his hair ruffled mercilessly.

Jack looked up at Cameron and he was grinning. "My boy's getting soft under you," he accused, his tone conversational despite the struggling, six-foot archeologist in his arms. "I couldn't have done this twelve months ago. Frankly, I'm disappointed."

"Sorry, Sir," Cameron apologized, coming to attention and looking serious. "I'll make sure we institute more rigorous hand to hand combat training and make sure to put emphasis on how to get out of your commanding officer's headlock."

"Are we there yet?" came Daniel's muffled complaint.

xxxxxx

"But we have lost contact with them before." The Daedelus' briefing room had been designed exactly the same as the Prometheus, plain clean lines and the minimum of adornments. Having been on more than a few Goa'uld motherships in his time, Jack appreciated the simplicity. He could see hints of Asgard influence in the space but the clean lines that spoke of practicality rather than finesse were all human.

"Yes, Sir, that's true. We weren't in a position to go and check on them however."

Jack looked across at Sam and his lip quirked. "Fair point. What I'm saying is that we shouldn't panic just yet. They survived for a year without any interference."

"That's true, and I trust Atlantis in the capable hands of Doctor Weir and Colonel Sheppard-" A tightness around Colonel Caldwell's eyes had Jack wondering _do you really_? "However the only possible reason that they would not have dialed Earth as planned would be because either the power from the ZPM was needed to boost the shields against bombardment or they were unable for some other reason."

"Very astute," Daniel muttered under his breath. Jack was the only one in the room to catch it and he gave Daniel a sharp kick in the shin under the table.

"The Wraith were still unaware of our continuing presence and we're just hoping that situation hasn't changed." Sam supplied.

"We still have the long range sensors so if the Wraith w_ere_ on their way, Atlantis would have had time to send a mayday, like last time." Caldwell tapped the desk with his fingers and then looked around the room. "If we had an incursion, I'd say it was through the 'gate. Security was not always strictly adhered to."

Jack blinked and then his eyes narrowed. "I'm sure Doctor Weir-"

"_Doctor_ Weir has on numerous occasions let teams through the 'gate when we could not verify whether or not they'd been compromised. I'm sorry, but I would rather trust procedure than gut instinct when it comes to the security of an entire outpost."

Jack got the feeling that the man before him had been just dying to say something similar for a long time and had just been waiting for the right audience. Jack remembered a time or two when he'd broken exactly the same rule.

A voice over the radio, pleading with him.

"_Sir, the Gate's gonna shut down and we won't be able to dial out again. …"_

"How about we see what's up before we start court-martialing people, eh?" Jack scrubbed a hand through his hair and pushed away from the conference room table. "We'll know what's up in about three hours."

"Sir, I want to repeat my previous position that leaving this outpost under civilian control is a mistake."

_Here we go, _thought Jack.

"Doctor Weir has the Pentagon's utmost confidence." Jack's tone was tired and both Sam and Teal'c looked at him. Daniel's brows had drawn down and Jack glanced at him, knowing he was dying to put in his two-cent's worth. Cameron's only response was to steeple his fingers under his chin.

"Sir, with all due respect, I would wager that your opinion in this matter would carry a great deal of weight-"

"Colonel, we're not having this conversation now," Jack snapped.

"Besides-" Jack knew that Daniel couldn't hold his tongue when the age-old civilian versus military argument was broached but Jack landed a heavy hand on his shoulder.

"We're not having this conversation now," he repeated, his tone one of quiet command.

xxxxxxx

Alone.

That word had meant a lot of things in his life, but never had it seemed so empty and so final. The single figure standing in Atlantis' control room sighed heavily, before reaching forward to activate the long-range communication device.

A familiar voice echoed through the empty depths of the city on the sea and he sighed again.

It wasn't much, but it was the only company he had.

_This is Doctor Elizabeth Weir. The City of Atlantis is under quarantine. Do not approach under any circumstances. I repeat, this is Doctor Elizabeth Weir. The City of Atlantis is under quarantine. Do not approach under any circumstances. I repeat…._


	3. Chapter 3

"This is Doctor Elizabeth Weir. The City of Atlantis is under quarantine. Do not approach under any circumstances. I repeat, this is Doctor Elizabeth Weir. The City of Atlantis is under quarantine. Do not approach under any circumstances. I repeat…".

"What the hell is that?" Jack had arrived on the bridge and was looking at Caldwell expectantly, a familiar voice echoing over the loudspeaker.

"It's a do-not-approach, Sir." Caldwell answered and Jack looked behind himself to Daniel and Teal'c, who had followed him in.

The message changed timbre and language and all looked at Daniel expectantly. He raised his eyebrows and circled a finger in the air. "French," he supplied. They listened to the message cycle through and change again and this time Daniel winced. "Okay, now that's someone murdering Ancient."

"How far out are we?" Jack asked. Caldwelll looked to one of his Lieutenants who turned in his chair.

"About an hour, Sir. We weren't sure what the problem was and didn't want to drop out of hyperspace right in the middle of a Wraith Armada."

"Smart," Jack acknowledged. The message had changed again and the guttural barking made everyone wince.

"Goa'uld." It was Teal'c who had identified it this time.

"Why Goa'uld?" Caldwell asked. Teal'c raised and eyebrow and Caldwell nodded. "Ah, right."

"Well, I certainly didn't spend 18 days cooped on this damn ship only to turn around and go home," Jack said, clapping his hands together.

xxxxxxx

When the large, reinforced doors that lead from the landing bay into Atlantis itself refused to open, Daniel turned to Jack and inclined his head. "I think it needs your special touch," Daniel sighed, mindful of the marines flanking him, silently glowering at his presence.

Daniel had heard the argument about why SG-1 should not be the first team between Caldwell and Jack had ended in a compromise which was why he now felt like he was entering the city with an entourage.

"You only use me for my gene," Jack grinned as he stepped forward, brushing a hand over the touchpad that Daniel had been working on for the last ten minutes. There was a hollow sound from deep within the walls and then the doors started to slide back.

"Cool," the marine on Daniel's right breathed and Daniel felt his annoyance at being babysat melt, just a little. A few seconds later, an arm was pushing him back and behind as the sound of a weapon being cocked from the darkness. Daniel squinted into the murkey depths of the entryway and could make out only the vague outline of a tall figure within. The marines, he and Jack all retreated a little way.

"Stand down!" the marine that had been awed only a few seconds earlier, snapped out. Jack stepped forward and around the man and Daniel heard the marine curse at his line of fire being blocked.

"Sheppard?"

The figure seemed to twitch and then lope forward. Daniel felt the marines surrounding him bristle but the lanky figure that emerged into the light of day was unmistakably the spiky-haired Colonel Sheppard. He slowed to a halt still a few careful feet away from the Daedelus group and raised a hand to shield his eyes as he squinted at them.

"General O'Neill?" His P-90 was still held loosely in one hand but was by his side. "Tell me I'm not hallucinating." John Sheppard's voice was tinged with hope and not a little bit of fear, as if the possibility of a daylight hallucination wasn't that far from being true.

"None other," Jack held his arms out, showing his own lowered weapon. Again, Daniel felt the marine's unease but just as John started forward again, Jack's weapon raised.

"Hold it there," Jack ordered and John came to a halt, looking mystified, but his face cleared a few seconds later.

"Ah, right, sorry. Lost my head there for a sec," He offered them a lopsided grin that didn't quite reach his eyes and Daniel thought that he had probably never seen anyone looking quite so… _worn out_.

"Colonel Espenez, how about two of your men keep Colonel Sheppard company here while we make a sweep of the major parts of the city," Jack ordered but a sound from John made them all turn back in his direction. He had one hand up and was backing towards the entry doors.

"We were broadcasting a do-not-approach message. It wasn't just for kicks you know."

"Don't you know stuff like that just makes people want to… approach?" Jack was trying for levity but Daniel noticed that he was advancing on Sheppard as quickly as the Colonel was retreating, and he hadn't dropped his weapon all the way. Daniel let a hand ghost down to his thigh holster.

"We've had an outbreak that we couldn't contain. I'm just hoping it's not too late for you and your guys to get the hell out of here." Sheppard was nearly through the large entryway and Daniel knew that Jack wouldn't let him get past it.

Sheppard's hand reached for the touchpad that Jack had only just activated and Jack's weapon raised again, the second time in as many minutes. "Don't," he said simply, his tone one of command. Sheppard automatically hesitated, the urge to obey so deeply ingrained that his hand had snatched away before he'd thought about it.

There was the whip-crack sound of a zat being fired and Sheppard grunted, a comical expression of annoyance on his face, before he dropped to the ground. Daniel looked up and around and saw Teal'c lowering the zat.

The Jaffa raised an eyebrow and nodded slightly.

Jack inclined his head back.

xxxxxx

Mindful of Sheppard's warning, if not the motivation behind it, the first strike group of marines had suited up in hasmat before entering the facility. Jack, Daniel and Sam had accompanied them but after checking the 'gate room, control room and most of the larger living spaces that would have been frequented, they found not another living soul.

They checked the jumper bay and according to the records they had had transmitted back to the SGC, a full compliment of ships was still present and accounted for.

"Okay, this is just spooking the hell out of me," one of the younger marines, a man named Bennet, intoned.

"I have to agree," Daniel was turning a slow circle back in the 'gate room.

The silence was oppressive.

"I'm not reading anything unusual, Sir." Sam supplied, checking the hand-held counter she was carrying. "If there was a bio-hazard then it might have dissapated by now, or was trasmitted from carrier to carrier, or is a physical contagion. I can't see any reason why we need to stay in hasmat."

"Good enough," Jack agreed and pulled his own head covering free, running a hand through his sweaty hair when he had it clear. "You and Daniel check the logs and see if you can find just what the hell is going on here. I'll go and have a chat to our solitary Sheppard."

"Yes, Sir."

xxxxxxx

John Sheppard had awoken in one of Atlantis' infirmary beds, and for a few blissful seconds he had thought that just maybe the events of the last few weeks had only been the result of a nasty concussion or a fever dream.

Jack O'Neill, leaning over him with eyebrows raised and a quizzical expression put paid to that idea.

The presence of restraints didn't help matters.

John sat up slowly, mindful of his tethered arms and went to rub a hand through his hair, only to find the movement restricted. He scowled. "I'm not dangeous. Right about now I'm the least of your problems."

"Mind telling us why it seems your bumping around Atlantis all by your lonesome?" Jack asked, dropping himself on to the infirmary bed opposite. John looked from the two marines guarding the infirmary doorway and back to Jack before answering.

"I'm not alone. Everyone's still here. I'm just the only one… _awake_."

Jack blinked.

xxxxxxx

"I'm not sure what I'm looking for," Daniel grumped, scrolling through screens and screens of files. Sam bumped his elbow good-naturedly.

"Look for anything with a date of the last couple of days or weeks." Daniel sneezed mightily and Sam grinned at him. "We're in a metal and glass city in the middle of the ocean. What could you possibly be allergic to here?"

Daniel glowered at her before turning back to the computer. "Dust," he grumped and sneezed again. He narrowed his eyes when Sam snorted in amusement.

"Shutup!"


	4. Chapter 4

"I'm not saying another word until you give that order, Sir."

Sheppard was sitting up on the infirmary bed, still restrained, but looking adamant although exhausted. He'd tried to cross his arms in defiance and had found his movement hampered and had instead dropped his arms to his sides, curling his fists.

"You have to tell us what's going on." Caldwell snapped and John's gaze ticked to him, his brows drawing down in annoyance.

"I don't have to tell you jack," he snapped and then looked at Jack when the older man raised his eyebrows quizzically. "Not _you_ Jack, the collective… ah crap. I don't have to tell you a good goddamn thing." Sheppard tried to rub his temple, found he couldn't and tugged on the restraints in annoyance.

Jack raised a hand to his ear and clicked on his radio. "Anyone currently on the Daedelus, consider yourselves restricted to the ship. Anyone already in the city is not to go back to the ship. That's an order." Sheppard looked placated and Caldwell incensed. Jack clicked off his radio and crossed his own arms. "There, now give me a good reason for doing that."

Sheppard sighed heavily; seemingly sinking into himself, as if winning that tiny battle had taken more out of him than he had left to give. "Carson recorded his findings before…" Sheppard looked pained for a moment, but took a breath and continued. "It's probably better you watch it. There's a datapad over there," Sheppard waved a hand towards what would have been Carson's desk. "You can plug it straight into any monitor."

Jack picked up the small black device Sheppard had indicated and looked at it. He glanced at Sheppard who nodded.

xxxxxx

"I've found where all the power's going." Sam caught Daniel yawning mightily and grinned at him. He snapped his mouth closed and struck an attentive pose that reminded her so much of Jack that she grinned harder.

"Wondering where the ZPM went?" Daniel raised eyebrows and Sam nodded.

"We're on bare minimum here and most of the city has been shut down. There are some sections we can't even get into and also, no shield. Colonel Sheppard couldn't have done this by himself." Sam ran a hand through her hair.

Daniel started when he realized there was someone standing directly behind him. Cameron grinned down at him and Daniel scowled back. "I hate when you do that," Daniel complained.

"Neither of you have your radios on," Cameron observed, flicking Daniel in his naked ear to get his point across.

"We were busy, and there's five marines below us, all with theirs on. If they started running we'd know to follow." Daniel sighed, rubbing his abused ear. "Also, just because Jack got me in a headlock on the Daedelus, doesn't give you permission to do the big brother torture as well."

"Just gonna have to fight back, then." Cameron challenged, making a comical martial arts gesture which involved flailing arms and a sideways kick. Daniel made to push himself away from the console he and Sam were at with a smirk but Sam touched his shoulder, halting him.

"We're working," she scolded and he sunk back into his chair with a guilty flush.

"Anyway," Cameron pulled a third chair up. "We've been given an order not to approach the Daedelus if we're already off it. Know what that's about?"

"No idea." Sam shrugged. "As I was telling Daniel, though, I've found where all the power is going but I can't tell what for. It's right in the bowels of the city and I'd like to check it out." Sam tapped the screen in front of her that was showing a two-dimensional schematic of the city. There were faint dots of colour spread around their immediate area, but one large glowing blob in the far right of the screen.

Cameron's radio clicked and he listened for a second, his brow furrowing. Daniel and Sam looked at each other, then at their earpieces and both reached out to snag them.

"There were people on the mainland, right?" Cameron asked.

"Yes, the Athosians," Sam agreed.

"According the MALP telemetry, there's no one there now."

Sam blinked. "What the hell happened here?"

xxxxxxx

Jack remembered meeting Doctor Carson Beckett briefly when the Atlantis mission was being put together. He'd liked the good-humoured brogue of the man immediately and had been sad to see that he was heading off instead of staying at the SGC. There was a kindness and a professional wit to the man that Jack found appealing.

The man on the screen before them bared little resemblance to the one he had once met.

Carson was rail thin and there were dark smudges under his eyes. His hair was mussed and as they watched, he ran his hands through it repeatedly, taking to tugging at it every now and again. If Jack thought Sheppard looked exhausted when they first encountered him, then the Doctor went a dimension beyond that.

The accent was barely recognizable through the scratchiness of the voice and that was the most jarring of all. Jack looked back at Sheppard and saw that the younger Colonel had turned his head slightly so he couldn't see the screen.

Jack didn't blame him.

There was no escaping the thick rattle under the Doctor's voice that betrayed that exhaustion was not the only reason his body was falling apart.

"Is it on?" Carson asked, looking at the person who was supposedly holding the data recorder. He must have gotten an affirmation because he squared his shoulders and looked directly at the screen. Carson cleared his throat but that set off a round of wracking coughs that he struggled to control. The data recorder image wobbled and dropped away but they heard a gruff "I'm fine Rodney, let's just get this done," and the image swung up again and centered on Carson who had recovered enough to go on.

"Three weeks ago, a mild case of the flu started making the rounds of the Atlantis personnel. We inoculated everyone and thought it would run its course. Being in such close quarters, I thought nothing of the rate of infection. I was mostly concerned that we expose any of the Athosians to a viral infection that they had not encountered before and therefore had no defense against. Trips to the mainland were halted after we evacuated Teyla Emmagen who was currently the only Athosian in Atlantis itself and, ofcourse, Ronon Dex." Jack could see that skin tighten around Carson's eyes and read what it meant.

_First mistake_

"About eighty percent of the people infected seemed to start recovering only about four days after initial symptoms and we thought the virus was dying out."

Jack looked back at Sheppard who was studying his restraints. Jack crossed the room and released the Colonel who looked at him with gratitude, before letting his head drop into his hands.

"We were wrong."


	5. Chapter 5

"We're checking out where all the power's going, Sir." Sam said into her radio and the 'Yeah, sure.' from Jack had sounded distracted. Sam had hesitated, but decided that if Sheppard were still bumping around Atlantis then whatever had happened would have pretty much been over.

Still, always expecting the worst, Sam made everyone get back into hasmat before they headed to the lower parts of the city. She'd plotted out a course for them that would take them through the sections that still had power and so were accessible.

Daniel, behind his mask, was snuffling and looking annoyed. "Just _what_ the hell am I allergic to around here?" he grumped and Sam patted him gently on the shoulder in sympathy. She thought it would be an awful twist of fate that the one place Daniel was dreaming about going to would make his allergies crank up so badly that he wouldn't be able to even think of coming back.

"Do we know what's at the base of Atlantis?" Espenez asked and Sam looked back at him, shrugging slightly.

"Should we not just ask Colonel Sheppard?" Teal'c intoned. He tugged at his hasmat suit every now and again. Times like these he almost missed the symbiote. He didn't like being at the mercy of outside elements.

"I just want to check it out. There's got to be something important for the shield to be down to power it. We'll be fine."

"Where have I heard _that_ before?" Cameron intoned, but his protests at what they were doing were coming a little late and Sam knew he was just as curious as all of them.

"All I could get from the schematic was that there is a room beneath Atlantis that pretty much runs the length and breadth of the city itself. I'm thinking there's something wrong with the ballast systems and something's been jerry-rigged to keep the city afloat. If that's the case I may be able to do something about it and get the ZPM back to powering the shield where it belongs."

"All _I_ could get from that schematic was that it was a schematic." Cameron snorted and Sam sighed.

"It's just a pity the transporters are down. It's going to take us about an hour to get down there at this rate."

"They have transporters?" Cameron's voice had gone high-pitched with excitement. "That's just so…scifi!"

Daniel stopped and waved a hand about himself. "We're in another _galaxy_ . That's not scifi enough for you?"

"Oh, right, sure. Keep forgetting." Cameron waved a dismissive hand and Daniel threw up his own in mock surrender.

"I don't remember requesting another snarky commander."

His bulky suit muted the shrug Cameron offered. "It's a job requirement."

xxxxxxx

"The virus has three discernable stages." Carson took a moment to sneeze mightily and then looked at the screen apologetically. Something was said that wasn't picked up because Carson was raising a hand. "No, I said I'm fine. Let's just get this done."

Sheppard had slid off the infirmary bed and was now leaning against the wall in the corner of the room, looking like he wanted nothing but to flee. Jack watched him out of the corner of his eye, knowing that he had probably had to sit through this recording more than once.

"The first, as I've described, is akin to the common flu virus. Fever, joint pain and lung infection. The second stage is a brief respite from this and we think the infected is on the mend. The third stage is the most dangerous, and not just for the patient. The closest thing I can diagnose is _Neurosyphilitic Disease. _The central nervous system is affected. For most this caused paralysis but in about fifteen percent of the cases we've had so far it has resulted in paresis."

There was a low chuckle from the corner of the room and both Jack and Caldwell looked at Sheppard sharply. "Sorry, Carson could never say _insanity_ like a normal person."

"Insanity?" Jack exclaimed.

"The paralysis of course was easy to spot. Unfortunately those otherwise affected, not so much." Carson continued and Jack and Caldwell looked to Sheppard again. He pushed away from the wall and his mouth thinned down in to a single slash.

"There were… some deaths," he stated, matter-of-factly.

"At first, we thought those with the ATA gene were not being infected. Although it wasn't the perfect solution, we started injecting all newcomers with the gene to give as many people a fighting chance as possible." Carson sniffled again. "As you can see though, it wasn't the magic bullet we were hoping for. The rate of infection was slower but it happened eventually. What we didn't realise at the time was that pretty much everyone in Atlantis was infected from the very first day the virus presented, everyone just had different rates of succumbing. As you can probably guess by that, both Teyla Emmagen and Ronon Dex had already been exposed when they were evacuated to the mainland."

Carson's whole face shut down in a neutral mask with this statement and Jack knew the expression well.

It was the face of a man who was blaming himself for catastrophe.

Jack reached forward and tapped the data recorder and the frame froze. "Enough! All I want to know is where the hell is everyone? Are you telling me they're all dead because I don't remember tripping over corpses on our way in here." Jack knew it was harsh but he had to get the shell-shocked expression of Sheppard's face and get the man functioning.

He knew the look of a man hanging on by his fingernails when he saw it.

Sheppard blinked for a second and then seemed to shake himself. He had been hugging his arms to his chest but they dropped away to his sides and his hands unclenched. He came to attention swiftly and naturally and Jack was glad, not for the first time, that he had pushed the man before him into taking the Atlantis posting.

He figured Sheppard probably wasn't particularly grateful at that very moment.

"About a month ago we moved onto the lower sections of the city for exploration. There'd been some structural damage when we first got here so it was top dangerous to explore without the shield in place because the risk of collapse and flooding was pretty high. The science guys found a huge expansive room underneath the city that housed hundreds and hundreds of stasis chambers. The city is capable of interstellar flight so it was only natural that something like this be present.

"We'd already had a couple of people turn violent and paranoid and while they'd eventually been restrained or worse, they'd also managed to do a fair bit of damage. The paralysis wasn't a walk in the park either. Internal organs would eventually fail and the medical team couldn't find any way of maintaining those people. Carson suggested we started putting people into stasis when they moved into the second stage and Elizabeth gave the order. At that point only about a third of the city were showing signs of infection and we still weren't sure that people couldn't recover on their own."

Sheppard rubbed a weary hand over his face. "We started getting reports of the Athosians being infected and so moved those that presented back to the city. The small trickle of sick turned into a flood."

"Isn't there anyone else still around?" Caldwell asked, incredulous.

Sheppard inclined his head and Jack sighed and tapped the data recorder again. "At this time, the only person in the whole city showing absolutely no signs of infection is Colonel Sheppard. From his interactions with Ancient technology, I can only guess that his genetic bond with the Ancients is stronger than the rest of us and it will only be a matter of time before he too presents symptoms. I only wish I had General O'Neill here as a control."

Jack snorted.

"When we lost about half the city, it was suggested that we put in a call for help." Sheppard offered, but Jack nodded, knowing what his response to that would have been in Elizabeth's position.

"You couldn't risk this getting out," he hazarded ad Sheppard nodded.

"Elizabeth, Rodney and I were the last ones awake. She recorded the message to broadcast and then we put her in to stasis. Rodney was fine up until about three days ago but he degenerated fast. By that time we'd had to hook the ZPM and all available naquada reactors into the stasis chambers."

"You're still fine." There was a note of accusation in Caldwell's voice and Sheppard rolled his eyes.

"Rodney was working on beefing up the naquada generators so we could take the ZPM back long enough to dial earth and get out a message but he got sick so quickly. He couldn't… " Sheppard took a second and his stance firmed. "We'd only hooked up the ZPM as an interim thing but it all happened so fast. It's only been four weeks since the first person sneezed."

Jack's mouth dropped open. "Four weeks?"

Sheppard nodded.

Jack suddenly remembered that he had given Sam permission to do something without really hearing what she was asking and thought that, without a doubt, she was headed to this stasis chamber Sheppard had described.

He figured he'd better warn her before –

"Holy crap, Jack, get down here!" Daniel's voice exclaimed in his ear and his exclamation was punctuated with a loud sneeze.

Daniel had been on an open channel and Jack looked quickly at Sheppard.

All colour had drained out of his face and Jack could almost hear what he was thinking.

_Not again. I can't go through this again. _


	6. Chapter 6

"Are you _angry_ about something?"

To keep up with Jack's purposeful stride, John had been reduced to jogging and he was very mindful that he had two minders behind him doing the same. Considering one of the virus' stages was seemingly a return back to full health right before insanity set in, John wasn't blaming O'Neill for wanting to keep two marines on his tail.

He was just thankful to be out of restraints.

"I'm fine." Jack threw over his shoulder and John risked reaching out and grabbing his elbow, halting his forward momentum. John heard the telltale click of zats opening behind him and held his hands up and away.

Jack turned on him. "What?"

"You look like you're pissed. I was just wondering why." John shrugged, risking the lowering of his hands when he heard the marines relax their stance.

"Maybe because it's Daniel every goddamn time!" Jack practically yelled, scrubbing a hand through his hair. John risked a glance back at the marines who were both intently staring at their shoes while still managing to keep Sheppard in their peripheral vision. He had to admit that the SGC always had the best people.

"Are you angry at Daniel or the world in general?" John leant a shoulder against the wall beside him and canted his head, studying the living legend before him. John had to admit he had never heard of General Jack O'Neill before the man turned up in McMurdoh in need of a pilot to the Antarctic base, but he'd heard stories since. Everyone who had ever worked with or had vague dealings with Jack was in awe of the man.

John just liked him because he had a tendency to disobey orders and mouth off to his superiors.

Sheppard could relate.

"Both," Jack sighed.

"Were you planning on going down there and yelling at Daniel?" John asked, raising an eyebrow.

"Yes." Jack confirmed

"That sounds like a good idea. He has no clue that he's possibly infected with an alien virus with no known cure and he's going to either become completely paralysed or nuts and you're going to let him know by marching up to him and screaming at him about… what exactly?"

Jack's shoulders slumped and all the fight went out of him. Worry flooded his face, so naked that it made Sheppard flinch. It was closed down only the briefest moment later but John had seen it and he had thought, _oh…_.

The anger was something to drown out all the other emotions and John could see Jack reach out for it mentally and reel it back into himself like a shield. "It's always Daniel. Kidnapped, drugged, abused and infected. That's our Dannyboy."

"I'm not sure that's his fault, Sir."

A sneeze issued behind them and both Jack and John turned as one, looking at the marine on the right named Peters. Donahue, the other, had immediately backed away from him.

Peters was holding his hands to his face like he could take the sneeze back, but his eyes showed above his splayed fingers, wide and terrified.

xxxxx

"Three hundred and eighteen." Espenez called out from his end of the stasis chamber.

"I get that too." Sam agreed, handing Daniel's notebook back to him.

"That's the Atlantis expedition and the Athosians." Cameron was standing in the middle of the chamber, as far as he could get from either side. He wasn't afraid to admit that the whole idea of stasis and the fact that they were practically standing in a tomb didn't sit well with him at all. "All of them," he added ominously.

"Pretty much beyond the fifth row," Sam indicated. "We start getting empty chambers. I'd say this is all of our guys and the Athosians accounted for."

"Why stasis though?" Daniel was peering into one of the chambers, trying to discern who the occupant was. He huffed and stood upright. "Found McKay," he said, tapping the clear window.

Sam grimaced. "Poor Rodney. He's claustrophobic. He would have hated getting in that thing."

"We don't know if he got in willingly, do we?" Cameron tapped the top of his P-90 thoughtfully. "Is there a release switch or something? We should get these people out."

"They were obviously put here for a reason." Espenez had jogged back to join them. "General O'Neill and Colonel Caldwell should be done interrogating Colonel Sheppard by now."

"Jack's on his way down. I thought he should see this for himself." Daniel indicated their surroundings with a wave of his hand.

"Carter! Gather everyone and get back up here now." Jack's voice barked in Sam's ear and she winced before tapping her earpiece to acknowledge.

Sam took a second to glance longingly at the ZPM and the Naquada generators hooked up to what she took for the main interface. "Sir, we haven't-"

"Now, Carter." Jack barked.

"Yes, Sir."

xxxxxx

Daniel sat at the conference room table, studying his hands. Sometimes, he wondered just how many times he could come back from the dead and the scars would still be present.

Along his little finger was a thin white line from when he'd slipped with a chisel.

Arcing across his palm was the faint squiggle of a burn from touching a Goa'uld device that wasn't as dormant as they had first thought.

In between the webbing of his ring and index finger on his right had was a twisted half moon from a roughly spun rope that he'd let slip through his fingers on Abydos.

Were these really his scars, earned and paid for with pain, or were they merely copies.

Sometimes Daniel wondered about the rest of himself.

Jack wrapped a hand on the table, getting Daniel's attention. "Well?" He raised his eyebrows, as if Daniel's opinion on what was happening was important. He supposed, to Jack, it was.

"Should I go into stasis now?" he asked, his voice hollow. Jack winced and looked at Sheppard who was standing in the corner of the room again. Sam reached a hand out across the table and brushed fingers against Daniel's forearm. He jerked it back and away and she looked at him with pained eyes. He grimaced. "Sorry, we don't know how it's transmitted."

"Frankly, from the rate of infection, Beckett was pretty sure it was airborne." Sheppard lifted one shoulder in a half shrug.

"I don't think we need to give up on you just yet." Sam's tone was light, but had a brittle edge to it.

Daniel's eyes swung to Sheppard. "Do I?" he repeated his question to the one person in the room that had lived through it.

"Most people we kept out until they hit the second stage. Carson went in as soon as he started showing flu symptoms, right after he recorded the message for you. He did that in case we needed… in case we needed to revive him for anything so he would have a little time."

"Smart guy." Cameron's voice issued from the other end of the room and Sheppard nodded in acknowledgement.

"We have the people we need on the Daedelus to figure this out. We just need to get some samples to them-"

"No!" Sheppard said sharply and all eyes turned to him. "I'm sorry, but haven't you noticed where you _are_? Atlantis boasted the best and brightest from pretty much any scientific field you could hope for, and they didn't find a thing. One by one they either died or got stuck in stasis for god knows how long and it all happened so fast that we shut up shop and prayed that no one would ever approach."

"Sheppard-" Jack held out his hands but John just glared at him.

"We don't know how communicable this thing is over distance or even if the people on the Daedelus are actually safe even though they haven't stepped foot in the city. Could you honestly risk them returning to Earth?"

"No." Jack said simply and with a finality that meant the thought had crossed his mind before that point in time.

All were quiet for a few moments, simply digesting what had just been said.

"Why are you fine?" Cameron asked.

"Does that really matter?" Sheppard sighed, scrubbing a hand through his hair.

Sam was tapping her chin in a way that both Jack and Daniel had come to love over the years and Cameron was learning to. It meant her brain was turning in a direction that would bring them salvation, although she herself didn't know it yet.

"It really does. Doctor Beckett was assuming the ATA gene retarded the advance of the disease so might not have been looking at the reason why you aren't succumbing at all. I'd say the chances of your body being naturally immune to this virus are pretty slim when every single other person exposed has succumbed. It's probably more likely to be environmental."

"Carter?" Jack prompted, sensing a spiel coming on and wanting to cut to the chase.

"Sorry, the question is, what has happened to you in your life that hasn't happened to a single other person on this base. Perhaps that's where we'll find our key."


	7. Chapter 7

"I'm not sure I'm comfortable with all this."

Both Jack and Daniel looked up at John Sheppard from their positions on either side of the conference table. Both had their legs up and a folder open before them.

"Any better ideas?" Jack offered, gesturing with the open folder. He was reading through John's medical file while Daniel was wading his way through the mission reports from the last year and a half of John's team looking for something unusual.

"Someone should edit Rodney McKay." Daniel grumbled, throwing another folder on the growing pile before him. "He had written about ten pages for everyone else's one."

"I thought you liked reading." Jack grinned and Daniel scowled at him.

"_No one_ can edit McKay." John added, unmistakable affection in his tone. He sank into the chair before him and drummed his fingers on the table's surface.

At Sam's suggestion, they were now going through the video footage and hard files that related to one Colonel John Sheppard. John was highly uncomfortable with how his every movement over his time in Atlantis was being scrutinized but he knew he couldn't argue with the logic. He agreed with Sam that the most likely cause of his apparent immunity had to be environmental. She and Espenez were going through the accumulated video footage that had mostly been shot by Rodney while Jack and Daniel had been relegated to going through his files.

John at least appreciated the small modicum of privacy he was afforded by the lower ranking marines not being included in the research.

Donahue had started showing symptoms shortly after Peters and they were all painfully aware of how much time they _didn't_ have. There had been no reports yet of anyone showing signs of the contagion on the Daedelus but that didn't mean it wouldn't happen. Caldwell was currently assigned going through the footage and Carson's notes on the illness itself. He had complained that he wasn't a doctor and he might miss something but Sam had shrugged and said that none of them were.

John took a moment to study Daniel while he was reading and noted how the archeologist had lost a lot of colour and there were dark smudges under his eyes. He coughed gently as he read and John knew it was only a matter of time before the coughs turned deep and racking as the virus progressed.

"You've had this before." Daniel jerked up, shaking one of the files.

"I think I'd remember that," John quipped dryly.

Daniel blinked at him for a second and then rubbed his forehead. "Not _this_ exactly, but there's been a disease unleashed in Atlantis before."

John sat up a little straighter. "Carson thought of that, but no one had been to any labs they weren't supposed to or broken anything. We were carrying out mostly structural exploration since getting the shield back up and working. The scientists had enough new toys to play with without hunting around for more just yet."

"He ruled out that it originated from offworld though?" Daniel's brow furrowed in a way that Jack recognized. Daniel had thought he had had a Eureka moment only to be deflated. It was usually either he or Sam that did the deflating.

"Yes. We hadn't had any teams go for about a month while we were working on repairing parts of the city. We had enough stores to last us and since the Daedelus could make trips back and forth now, we haven't needed to trade for food as much. Plus, the Athosians have some pretty healthy crops going."

Daniel dropped his head in his hands. "There's got to be something here," he sighed heavily, the sound more congested than usual. Jack winced to hear evidence of the virus that was slowly eating away at him.

Jack's radio clicked in his ear and he tapped it in acknowledgement.

"Sir, I think we've found something." Sam sounded both relieved and disturbed, a strange mix.

xxxxxx

"Don't watch anymore." John's voice was hollow and those gathered turned to him. Jack had to sympathise. The footage they were watching was hard to witness but Sam was right, it was important.

Carson Beckett's voice was describing what he was seeing as he rounded a figure in a dark room. The figure stood stock still, the very picture of agonized endurance. As the camera panned around and up, a face was revealed, although barely recognizable. Blue mottling covered the usually pale face and the eyes were flooded in black. Chitinous scale was halfway down the neck and disappeared under the collar. "Is that enough?" John's voice, when it issued from such an alien countenance, was jarring.

"I'm sorry Colonel, but could you lift your shirt for a moment." Carson's voice was truly pained, but he was a Doctor and a scientist. John's scaled and taloned hands edged up the hem of his black shirt and lifted it up and away, barring his chest. "As you can see," Carson's voice continued. "From the indentations on the abdomen it looks as if some of the ribs have merged to make a more solid shielding for the chest cavity. There is now scale covering about forty percent of the skin and the change is more extensive on his back." John dutifully turned and the ridge of his spine was clearly visible straining through the skin.

"Turn it off." Jack said, his eyes ticking to Sheppard and seeing that the other man had paled considerably.

"I hadn't actually watched this." John said, his hands knotting in the bottom of his shirt and twisting. "Carson wouldn't let me." A humourless chuckle issued from him. "I can see why."

"Don't you see?" Sam turned in her seat, trying to dampen the glitter of new discovery in her eyes and failing dismally. "You were infected with the retrovirus Doctor Carson was working on, after it had passed through another being and possibly mutated. This could be it."

"That's a big leap, Carter." Jack warned, but she flapped a dismissive hand at him.

"Did you find _anything_ else that could even remotely begin to explain why John is standing here completely unaffected by a virus that seems to have an otherwise one hundred percent mortality rate?" Sam looked at each of them in turn.

Jack shrugged. "No."

Sam took a breath and looked to John. "I need Doctor Beckett."

"He's in stasis. He's _infected_." Caldwell protested.

"You said it yourself, Doctor Beckett put himself in stasis only shortly after presenting symptoms in case we needed him. Give me a defunct naquada generator or a black hole and I'm your gal. I wouldn't even know how to begin with this." Sam spread her hands apologetically.

"We have Doctors-" Caldwell began but Jack waved a hand.

"No one has presented that's still on board the Daedelus. Could we risk it?" Sam had her hands clenched into tight fists. "Besides, with one of our Doctors you'd be starting from scratch. This retrovirus was _designed_ by Doctor Beckett. If it's the key, he's our best chance."

"Where's Jackson?" Cameron asked, noticing that they were now missing one member of their group.

Jack sighed heavily and scrubbed a hand over his face. "I'll find him. You guys… talk amongst yourselves."

xxxxxx

Atlantis might have been vast, but currently they were restricted to a very small part of it, so Jack found Daniel relatively quickly. When he found him, Daniel was standing at the railing of the 'gate room balcony, overlooking the ocean. Jack had a moment of dejavu. He'd found a depressed Daniel standing at a railing once before and he didn't want to repeat the experience.

He was reassured when Daniel turned at the sound of Jack stepping out onto the landing, but the relief was short lived when Jack noticed the look on Daniel's face.

"I'm feeling better." Daniel said, his voice small and resigned.


	8. Chapter 8

When Carson Beckett opened his eyes, it took him a few moments to get his bearings. The first thing he noticed was that the room he was in was extremely bright and considering he had specifically chosen a room in the Northern Tower of the city that was pitch black in the mornings, it was either the afternoon or he was somewhere else entirely. He knew something important had happened recently but his sleep-addled brain was having trouble supplying him with the necessary information.

The second thing was that he felt absolutely atrocious.

In a flood, Carson remembered the last four weeks.

"Ah, crap," he sighed.

A blonde head entered his field of vision, someone vaguely familiar but he couldn't reconcile with being Atlantis. "Hi Doctor Beckett," Samantha Carter said brightly.

"Christ, what the bloody hell are you doing here?" Carson exclaimed.

xxxxxxx

They were still on the balcony, but Jack had steered them away from the railing in what he hoped was a subtle gesture. Daniel was now standing safely against the city wall with Jack between him and the ocean, just where he liked to be.

"We have no idea how long the second stage lasts so I should-"

"No, Daniel." Jack winced with his words, not really wanting to have the conversation he was about to. It just seemed so... cold.

Daniel was blinking at him in that rapid fire way that meant he was trying to marry what Jack had just said with what he'd been _expecting_ Jack to say, and coming up short. "No? What no?"

"No, we're not putting you in stasis yet. We still have to search the Ancient archives for any reference to this virus and you're pretty much the fastest... well, the only Ancient reader we have."

"But the translation program-"

"I already asked Sam. In twenty four hours it will have translated a grand total of three percent of the total Ancient archive."

"I'm not going to be reading it any faster," Daniel remarked dryly, raising his eyebrows.

"The problem with the translation program is it's going to translate _everything_. We need you to basically read through and skim, try and find sections that might be appropriate. Basically find any research materials they might have on bio-weapons."

"Bio-weapons?" Daniel asked, incredulous. "This is the Ancients. It's not like they wanted to invent-"

"Christ Daniel, we treat the Ancients like this body of great and all-powerful beings, and sure, they are _now_, but then-" Jack held up a finger, stabbing it down towards the ground. "They were on the losing side of a war that had been going on for a lot of years. They'd tried all their conventional weapons and hiding behind their shields. Don't tell me they didn't try to come up with something that would wipe the Wraith out once and for all."

"Is this something we know, or your conjecture?" Daniel asked, tossing up between being pissed at Jack's assumptions, and admitting that it sounded all too feasible.

"Hey, my conjecture has always been pretty spot on if you'll recall," Jack answered sniffily and Daniel had to grin.

"Fine," he said, holding up his hands in surrender. "I guess we don't really have time to go with _facts_ here."

Jack scowled. "We may start out by barking up the wrong tree at first, but I don't know any other way to thin the forest, do you?"

Daniel raised an eyebrow. "I think that may be the oddest thing you've ever said."

"Give me a break, I'm tired and in about two days you're going to be insane. I'm feeling the pressure here."

"You know, I could just become-"

"Daniel, this is _you_. If there's a smaller percentage option, that's where you'll go."

Daniel opened his mouth and then closed it again with a snap. No matter how much he wanted to argue, he just couldn't.

xxxxxx

"Times like these I feel… useless, you know?" Cameron was pacing outside the infirmary both Peters and Donahue had now been sequestered into. As yet, no one else was showing symptoms of the virus but they all knew it was only a matter of time.

Teal'c raised an eyebrow. "How so?"

"Sam's doing research and Daniel's translating. I'm just…waiting."

"I admit, it is hard when we are forced to fight an enemy that will not show its face. Give me a warrior brandishing a weapon and I know how to fight him. With times such as these, all we can do is stand by our friends and be strong."

"Wow, you don't say much but when you do." Cameron chuckled.

"What always pained me was when the Goa'uld would abandon a world, but leave weapons behind that were just waiting to go off. Their evil propagated long after they left. On Chulack, we had explosive devices seeded around the larger temples that are still being found to this day."

Cameron was standing stock-still. He turned slowly to Teal'c and clapped the large Jaffa on the back. "I thought stating the obvious that everyone was overlooking was General O'Neill's trick."

"I thought talking nonsensically was." Teal'c shot back and Cameron laughed.

"I'll explain on the way."

xxxxxx

"What are you two doing?" Sam had entered the control room and although Daniel had the Ancient interface scrolling through possible entries, he wasn't looking at it.

Instead he was scowling at Jack.

"He was trying to think of a time where he wasn't the first one to get the alien plague." Jack smirked.

"You ate the drugged aphrodisiac cake." Daniel exclaimed triumphantly but Jack chuckled and shook his head.

"Drugged food doesn't count."

"Who says?" Daniel demanded, crossing his arms over his chest.

"I'm a General. I get to make up the rules."

Daniel threw up his hands and turned back to his work. A moment later he turned back with a grin. "The touched! The Neanderthal thing. Teal'c and I were the only ones immune."

Sam wanted to scold the two men before her, but knew they'd been working for hours and probably needed a break. Besides, she couldn't let what had just been said slide. "Daniel, that time you ended up infected _and_ kidnapped. I really don't think you want to use it as an example."

Daniel turned on her, hurt clearly on his face. "You're supposed to be on my side," he complained. "Us against Jack, we had a deal. We wrote a manifesto."

"You geek!" Jack was laughing now.

"I came to tell you that Doctor Beckett is awake and while he's in a foul mood, he's getting ready to get to work. Where's Colonel Sheppard?"

"He went for a run. He was climbing the walls down here, I thought he needed some space." Jack answered.

"Mines!" A voice echoed from the 'gate room below and Cameron appeared, taking the steps up to the control room two at a time. Teal'c followed in his wake at a much more casual jog.

"You know, we're looking for signs of crazy around here. You running around yelling random words isn't putting my mind at ease." Jack said, rising to meet Cameron.

"Sorry, Sir. The Ancients, they must have left a kind of biological time bomb or a mine."

Sam tapped Cameron on the shoulder. "Calm down and start from the beginning so we can catch up."

Cameron took a few deep breaths and looked to Teal'c, who inclined his head. "I've read a bunch of their mission reports, especially over the last month or so. I tend to retain things." Cameron tapped a finger to his temple.

"That's right, he does. He's read all of our old SG-1 mission reports and if you mention just one thing he'll start quoting it. It's… kinda freaky." Daniel canted his head and smiled disarmingly when Cameron treated him to a frown.

"Freakiness aside, it's also useful. Did anyone else think it was a big honking coincidence that they were opening new sections of the city right when this thing happened."

Sam smacked her forehead so loudly that all four men looked at her quizzically. "Of course. Sorry, explain." Cameron smiled at Sam, knowing she had already filled in the blanks herself, while Daniel and Jack were still looking at him in curiosity.

"They discovered the stasis chamber a week before the first case of this virus was recorded by Doctor Beckett. The engineers _forced open_ the doors instead of finding a way to override them. Doctor McKay practically wrote an essay on his mortification about that very fact."

"Are you saying-"

"They've triggered some kind of defense. This whole city was designed to fly like a ship. What's the one part of the ship you wouldn't want the enemy breaking in to?"

"The stasis chambers, because everyone in there would be defenseless." Daniel breathed.

"Not a very effective deterrent. They'd kill everyone in the stasis pods and get sick a week later?" Jack rubbed his jaw, playing devil's advocate.

"This virus wouldn't have been designed for _us_." Sam had picked up Cameron's thread and was running with it. "We need Doctor Beckett and we need any information on how this was designed and just why Beckett's retrovirus seems to have triggered an immunity in Colonel Sheppard."

Daniel turned back to the console he'd been working on. "I needed a place to start. Hopefully we have it."

"I'll track down Sheppard." Cameron volunteered, turning around and jogging off.

Teal'c followed Sam out of the control room while Jack stayed with Daniel.

"What can I do?" Jack offered.

"Coffee. I need coffee."


	9. Chapter 9

It had started as a tingling in the very tips of his fingers, six hours before.

Daniel had thought, _huh, for once I get to prove Jack wrong._

He kept working.

xxxxxxx

"It's quite ingenious really," Carson commented. He turned to the side and blew his nose expansively and then looked at Sam, who despite her best efforts, had leaned away from him. "Sorry, but you _did _wake me mid-flu."

"I'm sorry, go on." Sam scooted her chair closer to show that she wasn't afraid of Carson. She also knew that she probably already had the virus so being skittish around those who were showing signs wasn't going to help. She might as well wrap a scarf full of lavender around her face, for all the good it would do.

"I'm goin' on theory, mostly, but testing it on the Wraith tissue we had showed the infected samples had a much higher reaction than to the human cells we exposed. From our symptoms and from the way it reacts, I'd say this is a pretty nasty neurotoxin if you happen to be a Wraith. It would cause either the paralysis or… "

"Madness," Sam supplied, helpfully.

"Aye, or the _madness_ almost immediately. In humans, our bodies try to fight it off like any other infection and actually do quite a decent job of it, hence why we show flu-like symptoms."

"Why do we eventually succumb then?"

"Well, this virus was, from what we're supposing, _purpose built_. It's not like a naturally occurring illness. It was designed to mutate and compensate for any of the infected's natural immunities. The Wraith have a high rate of healing, especially if they're-" Carson grimaced. "Feeding. The virus would have had to keep attacking, long after normal viruses would have been killed off."

"Jesus, basically a virus that just won't quit once it's in your body." Sam rubbed her temple, thinking of the marines they had brought with them into the city. Thinking of Teal'c, Cameron and Jack and most especially Daniel, who looked like a good chance of being the first victim of their own.

"Aye, true, except in the case of Colonel Sheppard," Carson agreed, reaching across the desk and retrieving the sample of Sheppard's that he had taken. He held up a slide with a dot of Sheppard's blood, turning it in the light. "Here's our answer."

"You've figured it out?" Sam blinked.

Carson grimaced. "Not yet, but somehow this-" Carson tapped the slide with a finger, and then reached with his other hand for a vial of his own retrovirus. "Plus this, equals our answer."

Carson started coughing then, racking bursts that Sam thought sounded painful. She rubbed his back until they subsided. "Are you feeling any better?" she asked automatically, without remembering the implications of her question.

She winced but Carson grinned at her weakly. "Not at all, thank god," he replied dryly.

xxxxx

When Daniel's voice issued over the open channel with two simple words, everyone left what they were doing to come to the conference room, save the two marines that had become too ill to move.

"Found it," he'd simply said, and it was enough.

He'd explained that it was an experimental virus that the Ancients had been working on right towards the end of the war, before they'd abandoned their city. It had been made not as a vehicle to protect, but one to destroy. The hope was, that if the Wraith ever found Atlantis and tried to salvage her, that they would start with the stasis chambers, checking for survivors.

The virus would be triggered and although the Ancients were not there anymore, they would still land the final punch.

It had been named in the Ancient's database and Daniel had called it 'Babette's Plague' and no one had questioned it, until after.

Daniel was back at the Ancient terminal, looking for any and all references to the plague in the hopes that something would help Carson. Jack was swiveling in the chair next to him, back and forth, when he slowed to a halt and sat forward, elbows on his knees.

"Babette is a weird name for an Ancient," he remarked. He watched as a smile surfaced on Daniel's face.

"It's not what it's actually called. The proper name is Ba'beetene, but I thought I would save us both time by calling it what you'd end up calling it anyway."

Jack quirked an eyebrow.

Daniel reached over to pick up the pen he'd been making notes with but it slid from his fingers as soon as he touched it to the paper. "Crap," he sighed.

Jack had been swiveling again so had missed the pen dropping but heard the mild expletive. He turned back around and reached forward, tugging Daniel's sleeve.

"Everything alright?"

"I was hoping-" Daniel flushed and then indicated the balcony with a wave of his hand. "Can we go out for some air, just for a sec?"

"Sure." Jack's eyebrows had drawn down in concern, but he stood and trotted toward the balcony. Daniel was thankful that he had acquiesced without a backward glance as he had real trouble coming to his feet. He managed it and walked out to the balcony with as normal a gait as possible.

Jack once again stood between Daniel and the railing. Daniel tried to go around him, needing the railing for support by that time but Jack blocked his path, so instead Daniel had to make a grab for Jack's shirt front. Jack caught him awkwardly, not having expected six foot one of solid archeologist to actually _fall_ at him, and righted Daniel, pressing him up against one of the metal pillars that lined the balcony edge.

"Doc! Get down here!" he called raggedly.

"I was hoping to get through the translation and find something useful before I did this," Daniel apologized and Jack's expression darkened.

"How long have you been bad again?" he demanded.

"Only a few hours," Daniel said weakly.

"A few _hours_?" Jack exclaimed, inwardly cursing himself for not having watched Daniel closer, noticed _something_. Daniel raised his head and his eyes crinkled.

"Don't think you could have caught this," he sighed. "I became pretty proficient at hiding just how bad I was feeling under Janet."

"I should have noticed-"

"Why? You think you know me better than a woman who had had her hand in pretty much every orifice I have?"

Jack snorted despite himself. "No making jokes right now. You should have said something."

Daniel shrugged. "I had work to do."

"Daniel, that's an excuse for skipping lunch. Not for this."

"Can I just… I need to sit." Jack lowered Daniel gently to the balcony's tiled surface and Daniel hissed in relief.

"You just… can't keep doing this kind of thing." Jack lowered his head to Daniel's shoulder and breathed in deeply, trying to reign in the inexplicable _anger_ he was feeling at Daniel hiding his symptoms.

Daniel's hand came up with an effort and his fingers pushed through the hair at Jack's nape. Jack hitched in a breath and Daniel smiled. "There's something I've been meaning to tell you, for quite a while now," Daniel said and Jack raised his head to look into his eyes. "Just never seemed the right time."

"Whatever it is-" Jack began, but started when he heard the sound of booted feet approaching them.

When he turned back around, Daniel's eyes had closed.

_Me too,_ he finished.

xxxxxxx

"I _told_ him." Carson's voice issued from behind Jack, who was standing beside the stasis chamber Daniel had been laid in. He had a flat palm against the viewing plate, as if he could somehow push through the glass and let Daniel know that he was, above all else, terrified.

"Told him what?" Cameron asked and Jack was grateful, he wasn't sure he could speak right about then.

"That at the very first sign, and I mean _very first_ sign of the virus reoccurring, he was to come to me directly and go into stasis straight away."

"He wanted to keep working, I understand that," Cameron said.

Carson turned on him, throwing up his hands. "Most of these people were placed into stasis at the stage where they felt _better_. It was the only way to ensure recovery."

Jack turned slowly. "What do you mean?"

"Once we understood that no one actually _recovered_ from this, we took steps to give everyone the best chance at survival possible. Putting them in stasis in a weakened state is just… _madness_." Carson, once he had become comfortable with the word, was using it freely it seemed.

"Doc!" Cameron snapped, gripping Carson by the shoulder.

"There's about thirty people that were put in stasis in the final stages. Daniel makes thirty-one. The reason the number is so low is because we couldn't risk waiting until the final stage. I put myself in stasis at the very early end of the first stage because I'm going to have to go back in if I hit the second stage."

"Doc!" Both Jack and Cameron yelled this time.

"Fine! We needed people put into stasis as healthy as possible. The Ancient stasis isn't like your scifi movies where people are frozen. It slows everything down to an incremental rate, but the bodies still function. Putting someone into a state like this is like enforcing a coma."

Carson looked from Jack to Cameron.

"The very act of reviving them could kill them."

xxxxxx

"You heard?" Jack found Sam at the terminal Daniel had been working on. She looked up at him and her face was ashen.

"Yes, Sir."

"Find the way to stop this thing."

"Yes Sir."


	10. Chapter 10

"The 'don't ask, don't tell' thing really screws us, doesn't it?"

Jack hadn't seen Sheppard sitting in the shadows of the room he had retreated to. He was trying to stay out of the way while those that knew what they were doing actually worked on the problem. There was nothing here for him to shoot or blow up and he hated it. His fingers itched, wishing for something _physical_ he could rail against.

It seemed he could forever be standing between Daniel and the ocean, but he couldn't always hold back the tide.

"What are you doing up here?" Jack asked. They were both now in one of the very top rooms of one of the spires of Atlantis. The roof was glass and there was nothing but an expanse of stars overheard.

"Same as you, staying out of the way. They have my blood and they'll call me if they need more." Sheppard shrugged lazily. He was sitting on the floor with his back propped against a curved wall so that one of the clear overhead panels was directly in front of him. Moonlight played across his face, hiding his expression.

"I'll leave you be," Jack offered, but Sheppard raised a hand.

"No, stay if you like. Maybe both of us need someone to talk to before we go the non-induced-by-alien crazy."

"I'm fine," Jack said, but winced because he sounded anything but. He hated that he could remain stoic in the face of pretty much anything, except when in a room with a man who was practically a stranger but could pretty much see straight through him anyway.

"How long have you guys been together?" Sheppard asked as casually as if he was offering Jack a coffee. Jack started and his fists clenched.

"We've been friends for ten years." Jack said carefully.

"How about-"

"No," Jack snapped, cutting off Sheppard's further probing.

"No, never?" Sheppard was looking at him now, his head slightly canted and although Jack could now see his face properly, he still couldn't work out what expression the man was wearing.

"Of course not."

"Well, that's just nuts," Sheppard chuckled dryly.

"I'm sorry, but is it only me that realizes we're having a potentially career-ending conversation here?" Jack had backed up a few steps, as if putting distance between himself and Sheppard would stop the man seeing into the very heart of him.

"You risked career-ending the moment you looked at Doctor Jackson and thought, _hmmm, I'd like to screw that_."

Jack closed the necessary distance in order to hit Sheppard, but when the younger man stood up to meet him and simply raised his chin a little, expecting the punch with no intention of fighting back, Jack halted, fist clenched, elbow back. He grimaced and shook his head, dropping his anger like an old coat on the floor.

"Feel free to punish yourself, just don't try and make me do it," he grumbled.

Sheppard blinked and all the cocky self-assurance seemed to leak out of him. "I-"

"You have survivor's guilt. It's perfectly natural. You're the last man standing and if Doctor Beckett doesn't come up with the answer soon, you'll be the last man standing again."

"I'm sorry, Sir."

"So you should be. I resent the hell out of you dragging Daniel into your guilt party." Jack's voice was hard, but he touched a gentle hand to Sheppard's shoulder.

"You love him, right?" Sheppard asked.

For once in his life, Jack didn't hesitate. "Too much," he agreed.

"He doesn't know?"

"I've never actually _told_ him, but Daniel's pretty clever. He's probably worked it out. He probably doesn't know how long."

"How long?" Sheppard asked, his lip quirking in a half smile.

"You're a nosy son of a bitch, you know that?" Sheppard just shrugged and nodded. "Fine, leaving that boy on Abydos, all skinny and scruffy-haired was the hardest thing I've ever done."

xxxxxxx

Carson had something, and Sam didn't remember ever being so relieved.

"As I said, the human body was actually doing a pretty neat job of fighting this virus off on it's own. Unfortunately, fighting took a lot of energy and depleted the body to the point where the virus won out because it just kept attacking."

Sam nodded, her eyes fixed on a green vial Carson held in his fingers.

"There are two types of immunity. Natural immunity is created by the body's natural barriers, such as the skin, and protective substances in the mouth, the urinary tract, and on the eye surface. Another type of natural immunity is in the form of antibodies passed on from mother to child." Carson drummed the table with his fingers. "Then there's _acquired_ immunity. It develops through exposure to specific microorganisms, toxins or foreign tissue which are then remembered by the body's immune system."

Sam made a 'hurry up' gesture with her hand and Carson sighed. "You and Rodney, like two peas in a pod," he remarked and Sam grimaced.

"Anyway, because the Wraith's rate of recovery is so high, the virus was engineered with an acquired immunity suppressor, to basically stop the production of the specific antibodies needed to fight this thing. The science is a little beyond me, and if Colonel Sheppard hadn't been around, I might not have been able to do anything about it. It seems his exposure to the retrovirus boosted his production of these antibodies."

"So, stuff like antibiotics won't help?"

"Antibiotics are good for bacterial infections but nigh on useless for viral infection. Viruses traditionally have been difficult to treat because they replicate themselves using a body's own cells' enzymes and proteins."

Sam reached out and grabbed the green vial. "Tell me this is something and you're not just teasing me?"

"I've stripped back the retrovirus to its most basic form. This _should_ give us an immune booster similar to Sheppard's, without the unpleasant turning-into-a-bug side effects."

"Should?"

"It's all very experimental, but that's all we have at the moment."

Sam watched Carson for a few beats and then put the vial down on the table with a soft click. "You've already injected yourself, haven't you?" she asked slowly.

"Aye. I'm feeling better. Of course, I have no idea if that's because I've reached the second stage and the antivirus is completely ineffective," Carson grimaced.

"But in about six hours we'll know for sure. I can retest myself and if there is no presence of the virus, then we have a winner."

xxxxxx

Jack found Cameron and Teal'c sitting in the stasis room, close by Daniel's chamber. They'd found chairs from somewhere and had dragged them down. They were talking quietly, or at least Cameron was talking and Teal'c would occasionally nod or offer one or two words.

"What are you two doing down here?" Jack asked. He then noticed a third chair had been brought down and smiled when he sank into it.

"There should always be someone by our side when we are ill," Teal'c answered simply.

Jack touched his hand to the Jaffa's shoulder.

xxxxxx

Sam was dancing from foot to foot and Carson finally had to order her out of the room as he worked. He'd just drawn a sample of his own blood and was checking it for the presence of Babette's plague.

About ten minutes later, he stepped out into the hallway and Sam turned. She had Espenez beside her, looking almost as keen as she was. Espenez had started sneezing only an hour earlier.

"I'm clear." Carson announced. Sam squealed and threw her arms around the Scottish Doctor. "Alright-" he chuckled, breaking free. "Let's get you both inoculated."

Espenez held up a hand. "My guys first, please," he looked to Sam, who nodded.

xxxxxx

The sound of voices, after so long, filled Atlantis with life again. There was relief and not a few tears. All of this failed to carry down to the stasis rooms, where the final thirty-one people waited to be revived.

Carson had his full medical compliment, minus one nurse who was still in stasis who had hidden her own symptoms for as long as she could to keep working on others. A woman by the name of Beth Ambrose, who along with Daniel, concerned Carson the most.

Sam had been checking out the chambers and came up, rubbing at a patch of grease on her forehead and only succeeding in spreading it further rather than removing it. "There are clamps on the bottom of the chambers. You can remove them and transport them. It's only logical considering in an emergency you wouldn't want to wait for someone to revive before moving them. You'd want to be able to just get people out of here. I've been looking at the schematics as well, and there looks to be a retrieval system set up to move the chambers directly to the infirmary, kind of similar to how the Jumpers are moved to the 'gate room."

"Think you can activate it?" Carson asked.

"I'm sure we can figure it out, Carson." Rodney McKay sighed from behind Sam's shoulder. "If people had listened to me and not opened this room with a _crow bar_ maybe none of this would have happened," he couldn't help but add.

"Yes, Rodney," Carson sighed tiredly.

Sam chuckled.

xxxxxxx

He was on the balcony again.

Jack hated him being so close to the railing, and knew he should actually _tell_ Daniel that.

He supposed there were a lot of things he should have told him by now. Ten years was a long time to procrastinate, even for Jack O'Neill.

Daniel, as if sensing his presence, turned his head slightly. He was still a little drawn and pale from the whole experience, but Carson had reported that he was recovering fine. Jack wanted nothing more than to pull Daniel to himself, reassure his body that Daniel was fine. He knew it would be going a little fast though, zero to one hundred with no precursor in between.

"Do you think that's nine lives yet?" Daniel asked dryly and Jack chuckled.

"Can I just-?" Jack grasped Daniel's shoulders and shuffled him around until he was off the railing. Daniel swayed a little and Jack steadied him.

"What are you doing?" Daniel protested. "I'm not really steady here yet."

"I've got you," Jack reassured, his voice a little rough and his eyes darker. "Look, there's something… ah hell." Jack risked taking one hand away from Daniel to rub the back of his head. Daniel was watching him, curiosity plain on his features, like he was trying to decipher a particularly tricky passage of script.

"Whatever it is, Jack, just say it. I almost died again. We should probably stop walking on eggshells around each other."

"This thing, between us, it's not just all in my head. I mean, we've kind of had this conversation before."

Daniel blinked. "_When_ did we have this conversation?"

"Well, it wasn't in so many words."

"What words was it in? I think I would remember a conversation that involved you, me and the topic of having sex."

Jack flushed and suddenly found his boots fascinating. "Well, you remember the time I got a little too drunk and asked you to come back to my place?"

Daniel rubbed his temple. "Which time?" he asked.

"Uh… pretty much all of them."

Daniel was staring and Jack flushed darker. He forgot himself for a second and took his hands away from Daniel. The younger man fell against him heavily, hands bracing on Jack's shoulders. "Oh God, sorry," Jack raised his arms to help Daniel upright again but Daniel's hands snaked around Jack's neck instead and he pressed his lips to Jack's own. Jack opened his mouth to protest, but all that did was afford Daniel the opportunity to lick his way into Jack's mouth.

Jack made a noise that was halfway between a groan of resignation and a sigh of pleasure and then grasped Daniel around the waist, pressing him closer to his body. He'd been in the shower with the man, stark naked, but nothing had compared to the intimacy of being pressed bodily against him.

They broke off and Daniel was panting a little. Jack's eyes hooded with concern. "Are you okay?" he pressed backwards a little until Daniel was upright again.

"Sorry, I'm not a hundred percent, or I would be, you know-" Daniel made a gesture with his hand that was unmistakable. "_A hundred percent_."

Jack laughed. "It's probably better that you aren't. We're standing on a non-too-private balcony in a city that's filled with people again." Jack was a little breathless himself and he reached up and ran fingers through Daniel's hair, mussing it so Daniel looked more than a little wanton.

"Ten years huh?" Daniel breathed, letting Jack manhandle him until he was propped up against the metal pillar of the balcony.

"We both had to get to the point where we were indispensable," Jack shrugged and Daniel chuckled wryly.

"Plus, you had to get thousands of miles away," Daniel reminded him and Jack sighed heavily. He brought a hand up to Daniel's face and rubbed his thumb along Daniel's jaw line.

"We'll work it out," he said.

"But-"

"Daniel, we'll work it out," Jack repeated, more sternly this time.

xxxxx

Teal'c was standing by the balcony entrance. Every now and again some celebrating city citizen would approach and Teal'c would gently, but firmly, steer them in another direction.

Cameron approached, and tried to look past Teal'c, who sidestepped to block his view. "Watcha up to, T?" he asked.

"Absolutely nothing."

"Is that-?" Cameron started, getting a glimpse past Teal'c's broad shoulder.

"No." Teal'c raised an eyebrow.

"Oh, right." Cameron held up his hands, smirking. "Poor Daniel, he looks dead on his feet. Lucky the General is out there to help hold him up."

"Indeed."


End file.
